Discover Sage-Bionetworks/portals Open Source project

Bridge-iOS-SDK

The Synapse Repository Services project is the home of the JSON REST web services for Synapse.

Synapse-Repository-Services

An R package providing programmatic access to Synapse

CMSclassifier

synapser

rSynapseClient

The R programmatic interface to Synapse services

SynapseWebClient

The web client of the Synapse REST service core

JavaScript

schematic

Package for biomedical data model and metadata ingress management

Where OpenChallenges, Schematic, and other Sage open source apps are built

sage-monorepo

Participant-Centered Consent (PCC) Toolkit - exploring a visual approach to assisting the “informedness” part of informed consent for clinical studies.

PCC-Toolkit

mhealthtools

A modular R package for extracting features from mobile sensor data

MoleMapper

mhealthx is a software pipeline that automates feature extraction from mobile health data saved as a Synapse project (synapse.org).

mhealthx

Sage Bionetworks derived standards for annotating content in Synapse.

crcsc

CRC Subtyping Consortium

synapseAnnotations

BridgePF

DEPRECATED in favor of BridgeServer2

Validation and processing of GENIE files

Genie

Data and metadata ingress app

data_curator

dccvalidator

Metadata Validation for Data Coordinating Centers

aws-infra

Global Sage Bionetworks AWS Infrastructure

Jinja

rHDF5

Access HDF5 files from R. Based on a package originally authored by Roy Kuraisa, Wilson Lau and Jason Eglin at Merck & Co. that was donated to Sage Bionetworks.

mPower-sdata

scripts used for preparation of Nature Scientific Data submission and release of mPower data

metanetwork

Tumor-Deconvolution-Challenge-Workflow

Common Workflow Language

BridgeAppSDK

SDK for creating ResearchKit-based Bridge apps for iOS

To help quickly integrate your React app with the Synapse API backend

Synapse-React-Client

Stand-alone task modules for measuring cardiorespiratory fitness

CardiorespiratoryFitness-iOS

code for managing data coordinating operations through Synapse

syndccutils

Agora

Synapse documentation pages

synapseDocs

database-semaphore

rnaseqSim

PDBiomarkerChallenge

PDScores

url-signer

A simple Java Utility for Signing URLs

Code base for performing covariate adjustments and differential expression analysis of the RNAseq data from AMP-AD.

ampad-DiffExp

BridgeServer2

Bridge Server 2.0 running on Spring Boot

The design of the R Synapse client is getting crusty and difficult to maintain. Let's overhaul it!

rSynapseClientRewrite

Synapse-Stack-Builder

Project for building a complete Synapse Stack

This app enables exploration of the Drug-Target Explorer database.

polypharmacology-db

synapseformation

Client for using Synapse Formation templates.

Parkinson's disease clinical study app

mPower-2-Android

Drop-in Bridge-compatible CMS encryption implementation for use with AppCore.

CMSSupport

synapse-web-monorepo

Monorepo for Synapse Web projects

Ordering patients on smooth manifolds using lineage estimation tools

AMPAD_Lineage

This repository contains processing code for GENIE sponsored projects used for creating cBioPortal files

GENIE-Sponsored-Projects

dashboard

synAnnotationUtils

R package with code for AMPAD consortia manuscript

AMPAD

knit2synapse

Functionality to knit RMarkdown documents to Synapse wiki pages.

AMP-AD_Network_Analysis

location of analysis scripts for AMP-AD network working group

challengeutils

Synapse challenge utility functions

Code for linking a workflow engine to a Synapse evaluation queue

SynapseWorkflowHook

Scouring the Glioblastoma (GBM) TCGA expression data for molecular signatures indicative of survival benefit

Glioblastoma-Exploration

rare-disease-workflows

Workflows for processing rare disease data on Synapse.

Common Workflow Language

dermalNF

Code designed to annotate and process CTF-funded dermal NF samples. All available data and key analysis steps uploaded to http://www.synapse.org/dermalNF

mPower-2-iOS

Source code for the iOS version of the mPower 2 study app.

Basic structure of a R Shiny application for use on Synapse

SynapseShinyApp

challengerutils

Synapse R challenge utility functions. (wraps challengeutils)

mpowertools

feature extraction toolkit for mPower modules

SynapseWorkflowOrchestrator

Glue pipeline to export Bridge data as Parquet and CSV to Synapse

BridgeDownstream

cross-platform architecture for serializing and displaying assessments run on mobile devices and used in scientific research

AssessmentModelKMM

developer-handbook

sagethemes

Sage-branded plot themes

s3-synapse-sync

lightweight implementation of the Synapse Activity services, based on the PROV spec

prov-service

A workflow for exploring and analyzing RNA-seq data.

mPowerRerun

sageseqr

nvml-statsd

This Python project integrates the NVIDIA management library with statsd to report GPU metrics to a monitoring tool

List of repositories here that utilizes the Synapse clients

awesome-synapse

digitalHealth_RetentionAnalysis_PublicRelease

Analysis code for "Indicators of retention in remote digital health studies: A cross-study evaluation of 100,000 participants"

minidream-r-env

Resources for setting up and managing an RStudio environment for interactive mini-DREAM activities

Shell

mPower-Android

mPower for Android

A Kotlin Multiplatform Mobile Bridge client

BridgeClientKMM

Shared framework for ResearchKit app studying Parkinson's disease, developed by Sage Bionetworks and University of Rochester.

mPowerSDK

Kubernetes deployments on ibc EKS cluster

kubernetes-deployments

Dockerfile

NF_LandscapePaper_2019

This repository hosts all the code used to generate analyses and figures for the landscape paper

R package for Synapse utilities

synapserutils

bridge-analytics-template

Repository for streamlining Bridge Data ETL

Enable monitoring of updates or newly created entities in Synapse

synapsemonitor

The schema-to-pojo project was started because we wanted to programmatically generate the Plain Old Java Objects (POJOs) from JSON schemas. More specifically we wanted to use the generated POJOs as resources of the Synapse JSON REST web services API. Since we are using the POJOs as REST resources we also wanted an easy way to marsh instances to/from JSON. Lastly, we also wanted to use the generated POJOs in our Google Web Toolkit (GWT) client-side code and server side code. Thus the schema-to-pojo project was born. Learn more at the folllowing wiki:

schema-to-pojo

Hack for NF - NF Hackathon 2020

nfhackathon2020

Jupyter Notebook

covidrecoverycorps

This R package provides scoring mechanisms for computational challenges and implements the bayesBootLadderBoot approach for avoiding test data leakage.

challengescoring

stopadforms

synapsegenie

This package can deploy a AACR GENIE like project on Synapse and perform validation and processing of files.

In-progress and example CWL tools/workflows

STM-metaAnalysis-clearScience

agoradataprocessing

sage-workflows-sandbox

jccli

A jumpcloud command line interface application

Application for validating CRF mobile health modules for the iPhone.

CRFValidationApp-iOS

Common compute resources for Sage data scientists

shiny-module-gallery

mHealthIdentityConfounding

CommonCompute

Shell

csbc-pson-dcc

Data coordination resources for the NCI CSBC and PS-ON consortia

Ranking methodology of potential Driver genes using multi-view feature sets

EvidenceAggregatedDriverRanking